Micro midterm 2 : 8-13

Lecture 8 — Macromolecules and central dogma

How does RNA polymerase start transcription?

1. Sigma factor recognizes the promoter.

2. RNA polymerase binds to the promoter.

3. DNA opens.

4. RNA polymerase starts at the +1 site and makes RNA.

Remember: Sigma finds the start; RNA polymerase makes RNA.

What does the core part of RNA polymerase do? What about the sigma subunit?

What do the core enzyme and sigma factor do?

• Core enzyme: Makes RNA by adding RNA nucleotides.

• Sigma factor: Recognizes the promoter and helps RNA polymerase bind.

What are the promoter regions that are important for RNA polymerase binding? Explain the consequence of having imperfect matches to these “consensus” sequences.

3. What are the important promoter regions?

• -35 region: Helps RNA polymerase recognize the promoter.

• -10 region: Helps RNA polymerase bind and open the DNA.

• Consensus sequence: The most common or ideal sequence.

A better match to the consensus usually means stronger binding and more transcription. A poorer match usually means weaker binding and less transcription

Describe the process of transcriptional termination.

How does transcription stop?

RNA polymerase reaches a termination signal.

• Rho-independent: RNA forms a hairpin, RNA polymerase stalls, and the RNA is released.

• Rho-dependent: Rho protein helps stop transcription and release the RNA.

Remember: Hairpin = Rho-independent; Rho protein = Rho-dependent.

Explain at what sequence ribosomes bind mRNA, and whether a ribosome can bind at more than one site on an mRNA molecule.

Ribosomes bind to the Shine-Dalgarno (SD) sequence on bacterial mRNA. They start making protein at the AUG start codon.

Yes! Many ribosomes can read the same mRNA at the same time to make multiple proteins. This is called a polyribosome.

What would be the result (in terms of the produced protein) if RNA polymerase initiated transcription one base upstream of its normal starting point and why? What would be the result (in terms of the produced protein) if translation began one base upstream of its normal starting point and why?

If transcription starts 1 base early: The protein may stay the same because the ribosome can still start at the normal AUG start codon.

If translation starts 1 base early: The protein will likely be different because the ribosome reads 3 bases at a time. Starting 1 base early causes a frameshift, changing the amino acids.

Remember: Transcription = may stay the same. Translation = frameshift, different protein.

Discuss whether a polycistronic mRNA has multiple promoters, multiple ribosome binding sites, both or neither?

A polycistronic mRNA usually has one promoter and multiple ribosome-binding sites (SD sequences) because it contains multiple genes that make different proteins.

Remember: One promoter, many SD sites, many proteins.

1. Be able to draw a diagram of a piece of DNA that encodes a three gene operon, the produced mRNA(s), and the produced protein(s). Indicate where the following are: (i) promoter(s); (ii) transcriptional start site(s); (iii) -10 sequence(s); (iv) -35 sequence(s); (v) Shine Dalgarno sequence(s); (vi) transcriptional terminator(s).

Remember what each part does

• -35 and -10: Promoter regions.

• +1: Where transcription starts.

• SD: Where the ribosome binds.

• Terminator: Where transcription stops.

• 3 genes → 3 proteins.

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— Lecture 9_ DNA and transformation

Summarize the reactions during DNA replication initiation, elongation, and termination. Where does this occur in the chromosome? What about on a plasmid?

Initiation (START)

• DnaA opens the DNA at the origin of replication (oriC).

• DnaB unwinds the DNA.

• DnaC helps DnaB attach.

• Primase makes RNA primers.

2. Elongation (COPY)

• DNA polymerase III adds new DNA nucleotides.

• DNA is copied in the 5' → 3' direction.

• Leading strand = continuous copying.

• Lagging strand = copying in short pieces (Okazaki fragments).

• DNA ligase joins the fragments.

3. Termination (STOP)

• Replication forks meet.

• DNA replication stops.

• DNA ligase seals remaining gaps.

• Two DNA molecules are produced.

Where does replication start?

• Chromosome: Starts at one origin (oriC) and moves in two directions (bidirectional).

• Plasmid: Starts at its own origin of replication and copies separately from the chromosome.

Initiation (START)

• DnaA opens the DNA.

• DnaB unwinds the DNA.

• DnaC helps DnaB.

• Primase makes RNA primers.

2. Elongation (COPY)

• DNA polymerase III makes new DNA.

• Leading strand = continuous copying.

• Lagging strand = short pieces.

• DNA ligase joins the pieces.

3. Termination (STOP)

• Replication forks meet.

• DNA copying stops.

• Two DNA copies are made.

Where does replication start?

• Chromosome = starts at oriC (one origin).

• Plasmid = starts at its own origin.

Identify the roles of DnaA, DnaB, DnaC, Primase, DNA Pol III, SSB and gyrase during replication. How do you think the cell ensures that there is sufficient energy before replicating its DNA?Summarize DNA replication: initiation, elongation, and termination. Where does it happen in the chromosome? What about on a plasmid?

• DnaA: Opens the DNA.

• DnaB: Unzips the DNA.

• DnaC: Helps DnaB attach to the DNA.

• Primase: Makes a starter piece to begin copying.

• DNA Pol III: Builds the new DNA.

• SSB: Keeps the DNA strands apart.

• Gyrase: Relieves twisting in the DNA.

How does the cell make sure it has enough energy?

The cell checks its energy and nutrient levels. It needs enough energy (ATP) and DNA building blocks before copying its DNA. If it does not have enough, it can delay replication.

What does each protein do?

Protein	Simple job
DnaA	Opens DNA at the starting point
DnaB	Unzips DNA (helicase)
DnaC	Helps DnaB attach to DNA
Primase	Makes RNA primers
DNA Pol III	Builds the new DNA strand
SSB	Keeps DNA strands separated
Gyrase	Prevents DNA from twisting too much

2. How does the cell get enough energy?

• DNA replication needs energy (ATP).

• The cell checks if it has enough energy and nutrients.

• If energy is too low, the cell can delay DNA replication.

3. Easy way to remember

• DnaA = Opens

• DnaB = Unzips

• DnaC = Helps DnaB

• Primase = Starts with primer

• Pol III = Builds

• SSB = Separates

• Gyrase = Untwists

What is a mutation and why are they important for evolution? Explain how and why cells maintain a relatively low mutation rate. Are all mutations detrimental?

A mutation is a change in DNA. Mutations create differences between organisms and help evolution happen.

Cells check and repair DNA to prevent mistakes.

Not all mutations are bad. They can be helpful, harmful, or have no effect.

What is a point mutation? What is the difference between silent, nonsense, and missense mutations?

A point mutation is a change in one DNA base.

• Silent: No change in the amino acid.

• Missense: Changes one amino acid.

• Nonsense: Creates a stop signal, ending protein production early.

What effect does an insertion or deletion within a gene coding sequence have on the resultant protein? What’s the effect of these mutations if they occur within a promoter, a 5’ untranslated region, terminator, or ribosome binding site?

1. What effect does an insertion or deletion within a gene coding sequence have on the resultant protein?

It can change the protein by shifting the reading frame, which can change many amino acids.

2. What is the effect if these mutations occur within a promoter?

It can change how much RNA is made.

3. What is the effect if these mutations occur within a 5′ untranslated region (5′ UTR)?

It can affect how much protein is made.

4. What is the effect if these mutations occur within a terminator?

RNA production may not stop correctly.

5. What is the effect if these mutations occur within a ribosome binding site?

It can make it harder for the ribosome to start making a protein.

If E. coli was growing without any extra mutagens, would you expect its genome to have any mutations? How would mutagen exposure change this?

Yes, E. coli can have mutations naturally when DNA is copied. Mutagens, such as UV light and certain chemicals, increase the mutation rate by damaging DNA.

Summarize the ways in which prokaryotes exchange DNA. Define transformation, conjugation and transduction in prokaryotes. Do these words mean the same thing in eukaryotes?

Bacteria can get DNA in 3 ways:

1. Transformation: Bacteria pick up free DNA from the environment.

2. Conjugation: One bacterium transfers DNA to another through direct contact.

3. Transduction: A virus carries DNA from one bacterium to another.

Do these words mean the same thing in eukaryotes?

No. These terms can have different meanings in eukaryotes.

🧠 Easy way to remember:

• Transformation = Pick up DNA

• Conjugation = Contact

• Transduction = Virus carries DNA

How do plasmids move between bacteria during conjugation?

Answer: One bacterium connects to another using a pilus and transfers a copy of its plasmid (DNA).

🧠 Remember: Conjugation = bacteria connect and share DNA.

Describe the similarities and differences between transformation and conjugation

Similarities: Both allow bacteria to get new DNA.

Differences:

• Transformation: Bacteria pick up free DNA from the environment.

• Conjugation: Bacteria connect and transfer DNA to each other.

🧠 Remember: Transformation = pick up DNA. Conjugation = connect to share DNA.

What is the fate of plasmid DNA versus non-plasmid pieces of DNA that enter a new cell, if they are to be stably maintained? Why are these different?

Answer:

• Plasmid DNA: Must have its own origin of replication (ori) so it can copy itself.

• Non-plasmid DNA: Must join the cell’s chromosome to be copied and passed on.

Why are they different?

Plasmids can copy themselves separately, but non-plasmid DNA usually cannot copy itself independently.

🧠 Remember: Plasmid = copies itself. Non-plasmid DNA = joins the chromosome.

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— Lecture 10 Genetic regulation coordination of gene expression

Do prokaryotes more often control the amount of proteins produced or protein activity? Why? (what are 4 reasons for this)

Answer: Protein amount.

Bacteria usually control how much protein is made because:

1. Transcription and translation are coupled (happen together).

2. mRNA has a short lifespan (breaks down quickly).

3. Prokaryotes have operons, allowing them to control multiple genes together.

4. It saves energy because cells do not waste resources making unnecessary proteins.

When do they control protein activity?

• When they need a fast response.

• When a pathway needs to turn on or off quickly

Compare and contrast the strategies used by transcriptional activators and repressors. What aspects are the same? What aspects are different?

Activators = turn genes ON.

• Bind to DNA near the promoter.

• Help RNA polymerase bind to DNA.

• Increase transcription.

Repressors = turn genes OFF.

• Bind to DNA at or near the operator.

• Block RNA polymerase.

• Decrease transcription.

Similarities:

• Both bind to DNA.

• Both control transcription.

• Both help bacteria respond to their environment.

Difference: Activators increase transcription; repressors decrease transcription.

uestion: Explain how the lac operon is regulated, including the genes lacZ, lacY, lacA, and lacI. How is transcription controlled? Explain when LacI binds to the operator and how CAP activates the lac operon when glucose is absent.

Answer:

1. What is the lac operon?

The lac operon is a group of genes that helps bacteria use lactose (sugar) for energy.

2. What does each gene do?

• lacZ: Makes an enzyme that breaks down lactose.

• lacY: Helps bring lactose into the cell.

• lacA: unkown function

• lacI: Makes the repressor protein that turns the lac operon OFF.

3. How does LacI (repressor) work?

• No lactose: LacI binds to the operator and blocks transcription.

• Lactose present: Allolactose binds to LacI, changing its shape so it releases the operator.

• Now transcription can happen.

4. What is allolactose?

• Made from lactose by beta-galactosidase.

• Binds to LacI.

• Removes the repressor from the operator.

5. How does CAP work?

• Low glucose: cAMP levels increase.

• cAMP binds to CAP.

• CAP binds near the promoter.

• Helps RNA polymerase bind.

• Increases transcription.

6. What is cAMP?

• A molecule that binds to CAP.

• High glucose = low cAMP.

• Low glucose = high cAM

Condition	What happens?
No lactose	LacI blocks transcription.
Lactose present	Allolactose removes LacI.
High glucose	Low cAMP; CAP inactive.
Low glucose	High cAMP; CAP activates transcription.

MOST IMPORTANT EXAM SENTENCE:

The lac operon has HIGH transcription when lactose is present and glucose is absent. Allolactose removes the LacI repressor, and cAMP activates CAP, which helps RNA polymerase bind to the promoter.

Easy memory trick:

• Lactose = removes the block.

• Low glucose = activates CAP.

• Both together = HIGH gene expression.

What level of expression of the lac operon would you expect in the following conditions? Draw out the promoter structure for each condition to explain why. 

1. High glucose, high lactose

2. High glucose, no lactose

3. Low glucose, high lactose

4. Low glucose, no lactose

onditions	Expression	Why?
High glucose + high lactose	Low	LacI is off, but CAP is inactive.
High glucose + no lactose	OFF	LacI blocks the operator.
Low glucose + high lactose	HIGH	LacI releases operator; CAP activates.
Low glucose + no lactose	OFF	LacI blocks the operator.

Easy way to remember:

• Lactose controls the repressor.

• Glucose controls CAP.

• HIGH expression requires high lactose AND low glucose.

Explain the difference between a gene, operon, and regulon.

Term	Meaning
Gene	A section of DNA that makes a functional product.
Operon	A group of genes controlled by one promoter.
Regulon	Multiple genes or operons controlled by the same regulatory factor.

Remember:

• Gene = one DNA instruction.

• Operon = group of genes.

• Regulon = multiple operons controlled together.

Explain how sigma factors work. What does it recognize, why does this matter? What is a housekeeping sigma factor vs alternative sigma factor. What is the benefit of using sigma factors to regulate a regulon? Are there any limitations – what would be the problem if the cell only used sigma factors as the only way to regulate expression?

How do sigma factors work?

• Sigma factors help RNA polymerase recognize and bind to promoters on DNA.

• They help RNA polymerase start transcription.

2. What do sigma factors recognize?

• They recognize specific DNA sequences called promoters.

• Different sigma factors recognize different promoters.

• This allows different groups of genes to be turned ON.

3. What is a housekeeping sigma factor?

• Controls genes needed for everyday cell functions.

• Helps bacteria survive and grow normally.

4. What is an alternative sigma factor?

• Controls genes needed during special conditions.

• Examples: stress, starvation, or environmental changes.

5. What is the benefit of sigma factors regulating a regulon?

• One sigma factor can control many genes at once.

• Helps bacteria respond quickly to environmental changes.

• Allows multiple genes to turn ON together.

6. What are the limitations?

• Sigma factors are not very specific for controlling individual genes.

• If bacteria only used sigma factors, they could not control each gene separately.

• Bacteria also need activators and repressors for more precise control.

Short Answer:

• Sigma factors: Help RNA polymerase recognize promoters and start transcription.

• Recognize: Specific DNA promoter sequences.

• Housekeeping sigma: Controls everyday cell functions.

• Alternative sigma: Controls genes needed during stress or special conditions.

• Benefit: Turns ON many genes at once (regulon).

• Limitation: Cannot control individual genes as precisely, so cells also need activators and repressors.

Remember for the exam:

Sigma = finds promoters.

Housekeeping = normal conditions.

Alternative = special conditions.

Benefit = controls many genes.

Limitation = less specific control.

Scientists can alter the DNA in a promoter so that a transcriptional activator becomes a transcriptional repressor. Explain how this could be done.

• Change the activator's DNA binding site.

• Move the binding site so the activator blocks RNA polymerase.

• This prevents transcription.

• The activator now acts like a repressor.

Describe how a small RNA (sRNA) might lead to reduced protein amount in a bacterial cell.

• sRNA binds to mRNA.

• Blocks the ribosome from attaching.

• Translation cannot happen.

• Less protein is made.

What is the advantage of allosteric regulation? How can negative feedback regulate a biosynthetic pathway?

Short Answer:

1. Allosteric regulation:

• A molecule binds to an enzyme and changes its shape.

• Turns the enzyme ON or OFF.

• Advantage: Fast response and saves energy.

2. Negative feedback:

• The final product builds up.

• It shuts down an earlier enzyme in the pathway.

• Production slows down or stops.

Remember for the exam:

• Allosteric = changes enzyme shape.

• Negative feedback = too much product stops its own production.

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— Lecture 11: Succeeding in the environment

What is stress to a microbe? Give examples.

Stress: Anything that makes it difficult for a microbe to grow, survive, or function normally.

Examples:

• High temperature (heat)

• Low temperature (cold)

• High salt (salinity)

• High pressure

• Lack of nutrients

• Changes in pH

What are the characteristics of stress?

Stress is an environmental change that makes it harder for a microbe to grow or survive.

Examples include heat, cold, salt, pressure, and lack of food.

How do microbes respond to stress? What are the 4 general steps?

1. Sensing: Cell detects the change.

2. Signal transduction: Cell sends the signal.

3. Response: Cell changes its activities.

4. Adaptation: Cell adjusts to survive the stress.

Remember: Sense → Signal → Respond → Adapt.

Speculate why most of the microbial stress responses involve regulation of many genes at once.

Because stress affects many parts of the cell. The microbe needs to turn on or off many genes to survive.

Stress can affect many parts of a microbial cell at the same time. The cell must turn different genes ON or OFF together to protect itself, repair damage, and survive.

Easy to remember: Stress affects many cell functions, so microbes must regulate many genes to survive.

Outline the general pattern of signal transduction systems and two component systems. What is a histidine kinase? Response regulator? How do sensors normally work?

Signal transduction: How cells detect a signal and respond to it.

1. Sensing: Cell detects a change in the environment.

2. Signal transduction: Cell sends the signal.

3. Response: Cell changes its activity.

Two-component system: Uses two proteins to respond to environmental changes.

• Histidine kinase: Detects the signal and adds a phosphate to itself.

• Response regulator: Receives the phosphate and controls genes by binding to DNA.

• Sensors: Detect changes in the environment and often change shape to send a signal.

Easy way to remember:

• Histidine kinase = Detects.

• Response regulator = Controls genes.

• Signal transduction = Detect → Send → Respond.

How do bacteria sense a rise in temperature? What is the sensor? What is the response regulator? How do they activate the σΗ regulon? How do they turn it off? do it separately please

1. How do bacteria sense a rise in temperature?

Answer: Bacteria sense heat when proteins start to unfold.

2. What is the sensor?

Answer: DnaK detects unfolded proteins caused by heat.

3. What is the response regulator?

Answer: σH (sigma H) helps turn on heat shock genes.

4. How do they activate the σH regulon?

Answer: Heat causes DnaK to help unfolded proteins. This frees σH to turn ON heat shock genes.

5. How do they turn it off?

Answer: When the temperature returns to normal, DnaK binds σH again and stops the heat shock response.

Easy memory: Heat = genes ON. Normal temperature = genes OFF.

Almost all bacteria have a heat shock response. Define heat shock and speculate about the temperature that might cause heat shock for a microbe that grows optimally at 10C, a microbe that grows optimally at 30C, or a microbe that grows optimally at 60C.

Heat shock: A sudden increase in temperature that causes proteins to unfold or become damaged.

• Microbe that grows best at 10°C: A temperature increase above its normal range could cause heat shock.

• Microbe that grows best at 30°C: A sudden increase above 30°C could cause heat shock.

• Microbe that grows best at 60°C: A sudden increase above 60°C could cause heat shock.

Important: Heat shock depends on the microbe's normal growth temperature. It is not the same temperature for every bacterium.

Easy to remember: Heat shock = sudden temperature increase that stresses proteins.

Bacteria express different things during log phase and stationary phase. What kinds of genes would you expect to be expressed a) mostly during log phase, b) mostly during stationary phase c) similarly during both? Why?

a) Mostly during log phase:

• Genes for DNA replication.

• Genes for cell division.

• Genes for protein production.

• Genes for nutrient uptake.

Why? Bacteria are growing and dividing quickly.

b) Mostly during stationary phase:

• Stress-response genes.

• DNA repair genes.

• Survival genes.

• Genes that help conserve nutrients.

Why? Nutrients become limited, and bacteria focus on survival instead of rapid growth.

c) Similarly during both:

• Housekeeping genes.

• Genes needed for basic cell functions.

• Genes for maintaining the cell.

Why? Bacteria need basic cell functions during all growth phases.

Easy to remember:

• Log phase = Grow and divide.

• Stationary phase = Survive and protect.

• Both = Basic cell functions.

1. In the last few lectures, we’ve discussed several regulatory systems. Which is the most simple (least parts) to turn on? Which is the most complex?

   • Lactose utilization

   • σ^Η regulon / heat shock response

   • stationary phase

   • quorum sensing

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Most simple: Lactose utilization (lac operon)

• Uses a small number of regulatory proteins.

• Allolactose binds the repressor and allows the genes to turn ON.

Most complex: Stationary phase

• Uses many regulatory proteins and signals.

• Controls many genes at once to help bacteria survive stress and low nutrients.

Easy to remember:

• Lac operon = Simple gene regulation.

• Stationary phase = Complex regulation of many genes.

When an E. coli culture shifts between glucose and lactose utilization, a lag phase is observed. However, when E. coli is shifted from 37°C to 47°C, the growth rate continues swiftly but no lag is observed. Using your knowledge about how these systems are regulated, explain why.

• Glucose to lactose: Bacteria need time to make new enzymes to use lactose. This causes a lag phase.

• 37°C to 47°C: Bacteria already have proteins that help them respond to heat, so they respond quickly without a lag phase.

Easy to remember:

• Lactose = Needs time to make enzymes.

• Heat shock = Uses proteins already available.

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— lecture 12: Secretion and motility

What is the Sec system and how are proteins targeted there? Where is the signal sequence encoded? Does it matter if its at the N-terminus or C-terminus of the gene? Explain why.

Answer:

• Sec system: Moves proteins across the cell membrane.

• How are proteins targeted? A signal sequence directs the protein to the Sec system.

• Where is it encoded? In the gene that makes the protein.

• Does location matter? Yes. It is usually at the N-terminus (beginning) of the protein.

Why? The cell recognizes the signal early while the protein is being made, so it can send the protein to the membrane.

Remember: Sec = protein transport. Signal sequence = address label.

Compare and contrast the Sec and BAM systems. Are they interchangeable?

Sec system:

• Moves proteins across the inner (cytoplasmic) membrane.

• Helps transport proteins out of the cytoplasm.

BAM system:

- Helps insert and fold proteins into the outer membrane of Gram-negative bacteria.

Similarities:

- Both help move proteins to the correct place in the cell.

Are they interchangeable?

No. They have different jobs:

• Sec = Moves proteins across the inner membrane.

• BAM = Inserts proteins into the outer membrane.

Easy to remember: Sec moves proteins across; BAM builds the outer membrane.

Do you think the Sec system would be a good target for antibiotics? What about the secretion systems (T1SS – T7SS)? Explain your reasoning.

1. Do you think the Sec system would be a good target for antibiotics? What about the secretion systems (T1SS–T7SS)? Explain your reasoning.

Answer:

• Sec system: Yes. Blocking it could stop bacteria from moving important proteins across the cell membrane.

• Secretion systems (T1SS–T7SS): Yes. Blocking them could prevent bacteria from releasing proteins that help them infect or harm a host.

Why? These systems help bacteria survive and cause infections. Blocking them could make bacteria weaker.

Easy to remember:

• Sec = Blocks protein transport.

• T1SS–T7SS = Blocks protein secretion.

Compare and contrast the various secretion systems. What elements are shared between secretion systems? What elements are different? Why do you think there’s so many kinds of secretion systems?

Similarities:

• All secretion systems help bacteria move proteins out of the cell.

• They help proteins reach specific locations.

Differences:

• They use different proteins and structures.

• Some move proteins across one membrane, while others move proteins across multiple membranes.

• Some release proteins outside the cell, while others deliver proteins into other cells.

Why are there so many kinds?

Bacteria need different systems to transport different proteins and perform different jobs.

Easy to remember:

• Same = Move proteins.

• Different = Different structures and pathways.

• Many types = Different jobs.

What are chaperones and why are they needed in some secretion systems? Give two examples of chaperones that play a role in secretion. What do you think would happen if you deleted these factors?

• Chaperones: Proteins that help other proteins stay properly folded and prevent them from folding too early.

• Why are they needed? They help proteins travel safely through secretion systems.

Two examples:

1. SecB: Helps keep proteins unfolded so they can pass through the Sec system.

2. Type III secretion chaperones: Help stabilize proteins before they are secreted.

What happens if deleted?

Proteins may fold incorrectly or fail to be secreted.

Easy to remember: Chaperones = Protein helpers that help proteins get transported correctly.

What is chemotaxis? Can bacteria swim directly towards a chemoattractant?

• Chemotaxis: Bacteria move in response to chemicals.

• Chemoattractant: A chemical that attracts bacteria, such as nutrients.

Can bacteria swim directly toward it?

No. Bacteria cannot swim in a perfectly straight line toward a chemical. They move randomly but change their movement to spend more time swimming toward the chemical.

Easy to remember: Chemotaxis = Moving toward good chemicals or away from harmful chemicals.

Explain how CheA / CheY controls flagellar motion. How does this relate to a run vs tumble? Explain why the rotation direction of the flagella needs to be controlled.

:

• CheA: Adds phosphate to CheY.

• CheY: Controls the direction the flagella rotate.

Run vs. Tumble:

• Run: Flagella rotate counterclockwise (CCW), helping bacteria swim forward.

• Tumble: Flagella rotate clockwise (CW), causing bacteria to change direction.

Why control rotation?

Bacteria need to change direction to move toward food and away from harmful chemicals.

Easy to remember:

• Run = Swim forward.

• Tumble = Change direction.

• CheA activates CheY, which controls flagellar rotation.

Understand the different kinds of motility, and how these kinds of movement are achieved. (swimming, swarming, twitching, gliding, sliding)

1. Understand the different kinds of motility and how these kinds of movement are achieved.

1. Swimming

• Bacteria move through liquid.

• Uses rotating flagella.

2. Swarming

• Bacteria move together across a surface.

• Uses flagella.

3. Twitching

• Bacteria move in short steps across a surface.

• Uses pili that extend and retract.

4. Gliding

• Bacteria move smoothly across a surface.

• Uses special movement proteins or surface structures.

5. Sliding

• Bacteria spread across a surface.

• Uses growth and expansion, without special movement structures.

Easy way to remember

Motility	How it moves
Swimming	Flagella in liquid
Swarming	Flagella on surfaces
Twitching	Pili pull the cell
Gliding	Smooth surface movement
Sliding	Growth pushes cells outward

In lecture 4 we talked about gas vesicles and how they are an energetically favorable way for bacteria to stay near the surface of water. Based on what you learned in lecture 12, expand your answer for why is it more energetically expensive to swim than float. Your answer should include specifics about what it means to be "energetically expensive" (as learned previously) and what parts of swimming are expensive.

Why is it more energetically expensive to swim than float?

Answer:

Swimming is more energetically expensive because bacteria must use ATP (energy) to move their flagella and push themselves through water.

• Swimming: Uses energy to rotate flagella and move the cell.

• Floating: Gas vesicles help bacteria stay near the water's surface without constantly using energy to swim.

Why is it energetically expensive?

It means the cell must use more energy (ATP) to perform an activity.

Easy to remember:

• Swimming = Uses ATP to move flagella.

• Floating = Saves energy because the cell does not need to constantly swim.

Do you think there are organisms that use twitching to get to the surface of water? Why or why not?

Probably not. Twitching uses pili to pull bacteria across solid surfaces. It does not work well in open water.

Easy to remember: Twitching = Movement across surfaces, not through water.

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— Lecture 13: Gut Microbial Communities

1. What distinguishes commensal bacteria from mutualistic bacteria? What benefits does a microbe get from living in a host?

Answer:

• Commensal: Bacteria benefit, but the host is not affected.

• Mutualistic: Both the bacteria and host benefit.

What does the microbe get?

• Food (nutrients).

• A safe place to live.

• Warmth and moisture.

Easy way to remember:

• Commensal = one benefits.

• Mutualistic = both benefit.

There are about 100 bacterial cells in your intestine for every one bacterial cell on your skin. What is one possible reason for this difference in microbial density? What lifestyle changes might reverse this difference?

Answer:

• The intestine has more bacteria because it has plenty of food, moisture, and a warm environment for bacteria to grow.

• The skin is drier and exposed to the outside environment, so it usually has fewer bacteria.

• Lifestyle changes like diet, hygiene, and frequent handwashing or bathing can change the types and amounts of bacteria on the skin and in the gut.

What is one distinction between the gut anatomy of foregut fermenters versus omnivores?

Answer:

• Foregut fermenters: Have a large fermentation chamber (such as a rumen) before the small intestine. Microbes help break down plant material.

• Omnivores: Usually have a simpler stomach and rely more on enzymes to digest food.

Easy way to remember:

• Foregut fermenters = microbes digest food before the small intestine.

• Omnivores = digest a variety of foods using their digestive enzymes.

What features of the 16S rRNA gene make it useful for identifying bacteria in microbial community samples?

Answer:

• It has conserved regions that are similar in many bacteria. These allow scientists to use universal primers to copy the gene.

• It also has variable regions that differ between bacteria. These help scientists identify which bacteria are present.

Easy way to remember:

• Conserved = similar in bacteria.

• Variable = different between bacteria.

• Together, they help identify bacteria in a sample.

1. The most abundant bacterial species living in the average healthy adult human gut belong to which two phyla?

Answer:

1. Firmicutes (Bacillota)

2. Bacteroidetes (Bacteroidota)

Easy way to remember: Firmicutes + Bacteroidetes = the two major gut bacterial phyla.

How might you grow a gut bacterial species in the laboratory if it can’t tolerate oxygen? What could happen to your gut microbiota if you swallowed a device that continually released oxygen as it passed through your intestines?

• In the lab: Grow the bacteria in an oxygen-free environment (anaerobic conditions).

• In the gut: The oxygen-releasing device could harm bacteria that cannot tolerate oxygen and change the balance of the gut microbiota.

Easy way to remember:

• No oxygen = anaerobic bacteria can grow.

• More oxygen = oxygen-sensitive bacteria may decrease.